The editor file dialogs connect directly to SharePoint libraries. We do not set our own permissions and use the ones already set in the libraries. We are not sure if MOSS 2007 will allow you to set specific permissions on each file in a document library, but you can do a quick google search on that or ask your question in the MOSS 2007 forums on MSDN.
Another solution you can try is to have separate document libraries for separate groups - e.g. one library for sales, one for accounting, etc. Then you can set the permissions on each library so only the respective group of people can access the files inside it.
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